Starting /dee2/code/volunteer_pipeline.sh SRR11389769 current disk space = 1545999368192 free memory = 1425226728 SRR11389769 SRAfilesize d79329103126121c48d2837e025d971c SRR11389769.sra SRR11389769.sra file validated SRR11389769 is paired end SRR11389769 is conventional basespace SRR11389769 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389769_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 35-76 %GC 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.98125 32.0 32.0 32.0 32.0 32.0 2 30.9905 32.0 32.0 32.0 32.0 32.0 3 30.96475 32.0 32.0 32.0 32.0 32.0 4 31.06175 32.0 32.0 32.0 32.0 32.0 5 31.01625 32.0 32.0 32.0 32.0 32.0 6 34.1215 36.0 36.0 36.0 32.0 36.0 7 34.0555 36.0 36.0 36.0 32.0 36.0 8 33.9055 36.0 36.0 36.0 32.0 36.0 9 34.09875 36.0 36.0 36.0 32.0 36.0 10-11 33.93625 36.0 36.0 36.0 32.0 36.0 12-13 34.147125 36.0 36.0 36.0 32.0 36.0 14-15 34.083875 36.0 36.0 36.0 32.0 36.0 16-17 34.119625 36.0 36.0 36.0 32.0 36.0 18-19 34.04275 36.0 36.0 36.0 32.0 36.0 20-21 33.971875 36.0 36.0 36.0 32.0 36.0 22-23 33.9525 36.0 36.0 36.0 32.0 36.0 24-25 33.842625 36.0 36.0 36.0 32.0 36.0 26-27 33.617999999999995 36.0 36.0 36.0 29.5 36.0 28-29 33.644000000000005 36.0 36.0 36.0 32.0 36.0 30-31 33.464 36.0 36.0 36.0 27.0 36.0 32-33 33.417249999999996 36.0 36.0 36.0 27.0 36.0 34-35 33.42375 36.0 36.0 36.0 24.0 36.0 36-37 33.64875409010823 36.0 36.0 36.0 29.5 36.0 38-39 33.49307827837906 36.0 36.0 36.0 27.0 36.0 40-41 33.428265794110246 36.0 36.0 36.0 27.0 36.0 42-43 33.23496098665996 36.0 36.0 36.0 21.0 36.0 44-45 33.398375052500654 36.0 36.0 36.0 24.0 36.0 46-47 33.144763343403824 36.0 36.0 36.0 17.5 36.0 48-49 33.054632426988924 36.0 36.0 36.0 17.5 36.0 50-51 33.1210976837865 36.0 36.0 36.0 14.0 36.0 52-53 32.73016872324351 36.0 36.0 36.0 14.0 36.0 54-55 32.68849156383783 36.0 36.0 36.0 14.0 36.0 56-57 32.60412994208008 36.0 36.0 36.0 14.0 36.0 58-59 32.43276083955088 36.0 34.0 36.0 14.0 36.0 60-61 32.456527217741936 36.0 36.0 36.0 14.0 36.0 62-63 32.08102318548387 36.0 32.0 36.0 14.0 36.0 64-65 31.913136661623803 36.0 32.0 36.0 14.0 36.0 66-67 31.73628743177882 36.0 32.0 36.0 14.0 36.0 68-69 31.58055615124714 36.0 32.0 36.0 14.0 36.0 70-71 31.69465582457296 36.0 32.0 36.0 14.0 36.0 72-73 31.402108634725742 36.0 32.0 36.0 14.0 36.0 74-75 31.14659405827809 36.0 32.0 36.0 14.0 36.0 76 30.657579062159215 36.0 32.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 27.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 4.0 22 2.0 23 7.0 24 14.0 25 23.0 26 44.0 27 66.0 28 109.0 29 165.0 30 234.0 31 350.0 32 481.0 33 702.0 34 1036.0 35 736.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.1631419939577 13.36858006042296 11.555891238670695 33.91238670694864 2 23.382834130380065 15.756355398942864 35.590234080040275 25.2705763906368 3 22.652907123080794 22.703246916687643 22.980115781525296 31.663730178706267 4 28.970551220739992 26.554241127611377 20.2617669267556 24.21344072489303 5 25.2705763906368 30.45557513214196 23.231814749559526 21.042033727661718 6 22.45154794865341 31.789579662723384 24.79234835137176 20.966524037251446 7 17.115529826327712 23.634533098414295 38.43443241882708 20.815504656430907 8 19.50667002265291 23.156305059149258 30.35489554492827 26.98212937326957 9 20.51346589478983 21.771960734960988 31.68890007550969 26.025673294739494 10-11 21.721620941354143 31.449786055877173 23.659702995217717 23.168890007550967 12-13 23.43317392398691 22.92977598791845 27.334507928517493 26.302542159577147 14-15 22.892021142713315 25.91240875912409 27.321922980115783 23.87364711804682 16-17 23.697457840422853 25.09438711301284 25.98791844953436 25.220236597029956 18-19 22.376038258243142 25.660709791089857 26.768185250440474 25.195066700226533 20-21 23.231814749559526 26.919204631261014 25.786559275106974 24.06242134407249 22-23 23.785552479234834 26.931789579662723 25.58520010067959 23.697457840422853 24-25 23.080795368738986 26.466146488799396 24.817518248175183 25.635539894286435 26-27 21.70903599295243 27.032469166876417 26.126352881953185 25.132141958217975 28-29 22.892021142713315 25.547445255474454 26.41580669519255 25.144726906619685 30-31 22.552227535867104 25.962748552730936 26.2522023659703 25.232821545431666 32-33 22.45154794865341 26.529071230807954 25.396425874653914 25.622954945884725 34-35 23.307324439969797 26.126352881953185 25.52227535867103 25.044047319405994 36-37 22.920075519194462 26.44430459408433 25.588420390182502 25.047199496538703 38-39 23.064333375299007 26.111041168324313 25.292710562759662 25.53191489361702 40-41 22.28657768823974 25.686225132208513 27.171996978091162 24.85520020146059 42-43 23.700440528634363 25.475141598489614 25.752045311516675 25.072372561359344 44-45 22.794210195091253 25.43738200125865 26.431718061674008 25.336689741976087 46-47 23.107920916761113 24.93388741972044 26.142803173403856 25.815388490114593 48-49 22.727272727272727 24.930747922437675 26.857214807353312 25.48476454293629 50-51 22.440498677748394 25.173151995970283 26.545775091298324 25.840574234983 52-53 23.602015113350124 24.28211586901763 25.957178841309826 26.15869017632242 54-55 22.411186696900984 25.673973293020914 26.379440665154952 25.535399344923153 56-57 22.055674518201286 25.192089683839274 25.859680060461017 26.892555737498427 58-59 22.75018905974288 25.170153768590875 26.44315603730779 25.636501134358458 60-61 22.28665069960923 24.70692045884281 26.988528929786966 26.017899911761 62-63 22.76853252647504 24.319213313161875 27.69793242561775 25.214321734745337 64-65 23.707440100882724 23.745271122320304 26.9609079445145 25.586380832282472 66-67 22.826498422712934 24.26498422712934 26.20820189274448 26.700315457413247 68-69 23.00605754669359 24.91166077738516 25.946491670873296 26.135790005047955 70-71 23.487814117944183 25.31885339057962 24.96527339310519 26.228059098371006 72-73 23.61815415821501 24.721095334685597 26.026876267748477 25.633874239350913 74-75 23.954575818303272 22.191048764195056 27.708750835003336 26.14562458249833 76 27.08106143220647 0.0 38.38604143947656 34.532897128316975 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 27.0 1 13.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 1.0 17 1.5 18 15.0 19 24.5 20 20.5 21 20.5 22 27.0 23 28.0 24 21.0 25 18.0 26 24.5 27 43.5 28 44.5 29 32.5 30 32.5 31 41.5 32 67.0 33 88.0 34 81.0 35 84.5 36 104.0 37 120.5 38 135.5 39 143.0 40 155.5 41 160.5 42 155.0 43 171.0 44 182.5 45 179.0 46 188.0 47 192.0 48 188.5 49 178.5 50 172.0 51 149.5 52 128.5 53 126.0 54 118.0 55 111.0 56 95.5 57 89.0 58 90.5 59 92.5 60 97.0 61 93.5 62 84.0 63 79.5 64 75.0 65 70.5 66 68.0 67 66.5 68 65.0 69 53.5 70 40.5 71 35.0 72 43.5 73 41.5 74 26.5 75 23.5 76 22.5 77 18.0 78 13.5 79 10.5 80 10.0 81 9.5 82 7.5 83 7.0 84 5.5 85 4.5 86 3.0 87 1.0 88 0.5 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.7000000000000001 2 0.675 3 0.675 4 0.675 5 0.675 6 0.675 7 0.675 8 0.675 9 0.675 10-11 0.675 12-13 0.675 14-15 0.675 16-17 0.675 18-19 0.675 20-21 0.675 22-23 0.675 24-25 0.675 26-27 0.675 28-29 0.675 30-31 0.675 32-33 0.675 34-35 0.675 36-37 0.012584948401711553 38-39 0.03775484520513466 40-41 0.05033979360684621 42-43 0.012584948401711553 44-45 0.0 46-47 0.0377643504531722 48-49 0.025176233635448138 50-51 0.0377643504531722 52-53 0.02518257365902795 54-55 0.0503651473180559 56-57 0.03777386048854193 58-59 0.03779765654529419 60-61 0.03780241935483871 62-63 0.05040322580645161 64-65 0.02521432173474534 66-67 0.05044772354647496 68-69 0.025233409033560434 70-71 0.012626262626262626 72-73 0.025348542458808618 74-75 0.01335826876836762 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 27.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 1.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 51 1.0 52 0.0 53 0.0 54 0.0 55 0.0 56 0.0 57 2.0 58 1.0 59 0.0 60 0.0 61 0.0 62 0.0 63 2.0 64 0.0 65 1.0 66 1.0 67 0.0 68 2.0 69 0.0 70 4.0 71 5.0 72 16.0 73 64.0 74 260.0 75 862.0 76 2751.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.25 #Duplication Level Percentage of deduplicated Percentage of total 1 97.16180371352785 91.57499999999999 2 1.936339522546419 3.65 3 0.5039787798408488 1.425 4 0.10610079575596816 0.4 5 0.07957559681697612 0.375 6 0.02652519893899204 0.15 7 0.0 0.0 8 0.02652519893899204 0.2 9 0.05305039787798408 0.44999999999999996 >10 0.10610079575596816 1.775 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 27 0.675 No Hit GCCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATT 22 0.5499999999999999 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 12 0.3 No Hit CCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTT 10 0.25 No Hit GTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTA 9 0.22499999999999998 No Hit GAAGAATTACTGCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTTC 9 0.22499999999999998 No Hit ATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTCTTCATATT 8 0.2 No Hit GCGCGAACTCGAATTTGATCGCCTTCCATACTTCACAAGCTGCGGCTAGT 6 0.15 No Hit CTTCCATACTTCACAAGCTGCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACG 5 0.125 No Hit CTTCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGA 5 0.125 No Hit AATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.025 0.0 0.0 0.0 0.0 23 0.025 0.0 0.0 0.0 0.0 24 0.025 0.0 0.0 0.0 0.0 25 0.025 0.0 0.0 0.0 0.0 26 0.025 0.0 0.0 0.0 0.0 27 0.05 0.0 0.0 0.0 0.0 28 0.05 0.0 0.0 0.0 0.0 29 0.05 0.0 0.0 0.0 0.0 30 0.05 0.0 0.0 0.0 0.0 31 0.05 0.0 0.0 0.0 0.0 32 0.05 0.0 0.0 0.0 0.0 33 0.05 0.0 0.0 0.0 0.0 34 0.05 0.0 0.0 0.0 0.0 35 0.05 0.0 0.0 0.0 0.0 36 0.05 0.0 0.0 0.0 0.0 37 0.05 0.0 0.0 0.0 0.0 38 0.05 0.0 0.0 0.0 0.0 39 0.05 0.0 0.0 0.0 0.0 40 0.05 0.0 0.0 0.0 0.0 41 0.05 0.0 0.0 0.0 0.0 42 0.05 0.0 0.0 0.0 0.0 43 0.05 0.0 0.0 0.0 0.0 44 0.05 0.0 0.0 0.0 0.0 45 0.05 0.0 0.0 0.0 0.0 46 0.05 0.0 0.0 0.0 0.0 47 0.05 0.0 0.0 0.0 0.0 48 0.05 0.0 0.0 0.0 0.0 49 0.05 0.0 0.0 0.0 0.0 50 0.05 0.0 0.0 0.0 0.0 51 0.05 0.0 0.0 0.0 0.0 52 0.05 0.0 0.0 0.0 0.0 53 0.05 0.0 0.0 0.0 0.0 54 0.05 0.0 0.0 0.0 0.0 55 0.05 0.0 0.0 0.0 0.0 56 0.05 0.0 0.0 0.0 0.0 57 0.05 0.0 0.0 0.0 0.0 58 0.05 0.0 0.0 0.0 0.0 59 0.05 0.0 0.0 0.0 0.0 60 0.05 0.0 0.0 0.0 0.0 61 0.05 0.0 0.0 0.0 0.0 62 0.05 0.0 0.0 0.0 0.0 63 0.05 0.0 0.0 0.0 0.0 64 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR11389769 read2 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389769_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 35-76 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.6175 32.0 32.0 32.0 32.0 32.0 2 30.34425 32.0 32.0 32.0 32.0 32.0 3 30.135 32.0 32.0 32.0 21.0 32.0 4 30.064 32.0 32.0 32.0 21.0 32.0 5 30.2885 32.0 32.0 32.0 21.0 32.0 6 33.25875 36.0 36.0 36.0 21.0 36.0 7 33.417 36.0 36.0 36.0 27.0 36.0 8 33.4195 36.0 36.0 36.0 21.0 36.0 9 33.34025 36.0 36.0 36.0 21.0 36.0 10-11 33.457625 36.0 36.0 36.0 26.5 36.0 12-13 33.4065 36.0 36.0 36.0 21.0 36.0 14-15 33.251625 36.0 36.0 36.0 24.0 36.0 16-17 33.107875 36.0 36.0 36.0 21.0 36.0 18-19 33.289375 36.0 36.0 36.0 21.0 36.0 20-21 33.112125 36.0 36.0 36.0 21.0 36.0 22-23 33.050250000000005 36.0 36.0 36.0 17.5 36.0 24-25 33.076875 36.0 36.0 36.0 21.0 36.0 26-27 32.895875000000004 36.0 36.0 36.0 14.0 36.0 28-29 32.9775 36.0 36.0 36.0 17.5 36.0 30-31 32.81725 36.0 36.0 36.0 14.0 36.0 32-33 32.67775 36.0 36.0 36.0 14.0 36.0 34-35 32.560500000000005 36.0 36.0 36.0 14.0 36.0 36-37 32.903584048460374 36.0 36.0 36.0 14.0 36.0 38-39 32.827344721840575 36.0 36.0 36.0 14.0 36.0 40-41 32.67129512749305 36.0 36.0 36.0 14.0 36.0 42-43 32.66965412774552 36.0 36.0 36.0 14.0 36.0 44-45 32.504216967707876 36.0 36.0 36.0 14.0 36.0 46-47 32.41982323232324 36.0 36.0 36.0 14.0 36.0 48-49 32.323611111111106 36.0 34.0 36.0 14.0 36.0 50-51 32.18055555555556 36.0 32.0 36.0 14.0 36.0 52-53 32.00593584238444 36.0 32.0 36.0 14.0 36.0 54-55 31.735539277595354 36.0 32.0 36.0 14.0 36.0 56-57 32.11101288204092 36.0 32.0 36.0 14.0 36.0 58-59 31.39414277931648 36.0 32.0 36.0 14.0 36.0 60-61 31.318377148634987 36.0 32.0 36.0 14.0 36.0 62-63 31.272118301314457 36.0 32.0 36.0 14.0 36.0 64-65 31.313606474456247 36.0 32.0 36.0 14.0 36.0 66-67 30.998976742678785 36.0 32.0 36.0 14.0 36.0 68-69 30.982382918274823 36.0 32.0 36.0 14.0 36.0 70-71 30.668831577829728 36.0 29.5 36.0 14.0 36.0 72-73 30.8004466819741 36.0 32.0 36.0 14.0 36.0 74-75 30.57997817527076 36.0 27.0 36.0 14.0 36.0 76 29.384885079859757 32.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 38.0 3 0.0 4 2.0 5 0.0 6 2.0 7 0.0 8 1.0 9 0.0 10 0.0 11 0.0 12 2.0 13 1.0 14 0.0 15 5.0 16 10.0 17 8.0 18 7.0 19 5.0 20 12.0 21 11.0 22 16.0 23 27.0 24 38.0 25 48.0 26 74.0 27 117.0 28 147.0 29 205.0 30 220.0 31 329.0 32 461.0 33 651.0 34 934.0 35 629.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.52007068921989 19.89396617015905 11.613228982580157 27.972734158040897 2 29.790456955314315 23.12547336531179 27.720272658419592 19.363797020954305 3 25.340737001514384 27.8899545683998 21.37809187279152 25.391216557294292 4 28.142352347299344 32.83695103483089 17.84452296819788 21.176173649671885 5 27.99091367995962 33.61938414941948 18.34931852599697 20.040383644623926 6 22.690560323069157 34.856133266027264 22.135285209490156 20.318021201413426 7 22.090381216864426 17.041151224438273 36.531178995203234 24.337288563494067 8 24.432104997476024 22.387682988389702 24.331145885916204 28.84906612821807 9 25.580808080808083 23.762626262626263 24.393939393939394 26.262626262626267 10-11 27.23253757736516 28.93772893772894 19.893899204244033 23.935834280661865 12-13 27.890812586882348 21.711108302792873 23.505623657272842 26.892455453051937 14-15 26.181127295756806 25.0538315389487 24.965167827739077 23.799873337555415 16-17 27.393617021276594 25.633232016210737 22.720364741641337 24.25278622087133 18-19 27.010622154779966 24.405665149215984 23.912493677288822 24.671219018715227 20-21 27.00582131106049 26.069349531764107 23.335864338142244 23.588964819033155 22-23 26.363751423870397 25.64232375648652 23.857739526642195 24.136185293000885 24-25 26.61188369152971 26.257901390644754 22.68015170670038 24.45006321112516 26-27 26.367088607594937 25.531645569620252 23.481012658227847 24.620253164556964 28-29 26.550240445456847 25.411288281447735 22.943558592761327 25.09491268033409 30-31 25.411288281447735 26.60086054163503 23.993925588458616 23.993925588458616 32-33 26.800860868464362 25.00316495758957 24.395493100392454 23.800481073553613 34-35 26.363751423870397 26.022022528793826 24.427287685103153 23.186938362232627 36-37 25.848101265822788 25.29113924050633 24.68354430379747 24.17721518987342 38-39 25.848101265822788 26.101265822784807 24.29113924050633 23.759493670886076 40-41 26.285135477336034 25.90529247910863 24.006077487971638 23.803494555583693 42-43 26.48511716276124 26.852438252058263 23.115896136795442 23.546548448385053 44-45 26.2678639180473 26.25521689642089 23.068167446566335 24.408751738965474 46-47 25.715008858516832 26.44900025310048 23.880030372057707 23.955960516324982 48-49 26.50709219858156 24.835359675785206 24.138804457953395 24.51874366767984 50-51 26.091357712261164 26.28115905352398 23.69986081234974 23.927622421865113 52-53 26.058920217473762 27.133645214312807 22.45543052218991 24.352004046023517 54-55 26.049570055639858 26.795649974709157 23.64693980778958 23.507840161861406 56-57 25.61638639524592 25.148564926033636 23.795675812365662 25.439372866354788 58-59 26.646403242147926 25.36727456940223 23.898176291793312 24.088145896656535 60-61 26.2770946888072 25.87146659906199 23.61516034985423 24.236278362276586 62-63 26.247151177513295 26.424411243352747 23.62623448974424 23.70220308938972 64-65 26.098518424718247 25.617323034063567 23.312650373559578 24.971508167658605 66-67 25.180585477125838 26.587251298948168 23.165631732353315 25.06653149157268 68-69 25.754119138149555 26.134347275031683 24.32192648922687 23.78960709759189 70-71 26.05768009147503 25.26997840172786 24.507686443908018 24.164655062889086 72-73 25.13389441469013 26.421831165519 24.22851313440449 24.21576128538638 74-75 26.246116439281376 23.382412535458595 25.63825476158314 24.733216263676887 76 27.077643386656263 0.0 36.9879047990636 35.93445181428014 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 38.0 1 19.0 2 0.0 3 0.5 4 1.0 5 1.0 6 0.5 7 1.0 8 2.0 9 2.0 10 1.0 11 0.0 12 0.0 13 0.0 14 2.0 15 4.0 16 4.0 17 4.0 18 9.5 19 12.5 20 12.5 21 14.5 22 15.5 23 14.0 24 14.0 25 18.5 26 20.5 27 18.0 28 20.0 29 28.5 30 39.5 31 55.5 32 67.5 33 70.5 34 61.5 35 70.5 36 87.5 37 90.5 38 101.5 39 103.0 40 114.5 41 138.0 42 140.0 43 158.0 44 178.0 45 174.0 46 169.0 47 173.0 48 178.5 49 171.0 50 166.5 51 166.5 52 143.0 53 126.0 54 135.5 55 118.5 56 104.5 57 118.5 58 126.5 59 119.0 60 114.0 61 114.5 62 113.0 63 102.0 64 88.5 65 83.0 66 77.0 67 73.0 68 64.0 69 62.0 70 66.0 71 60.5 72 52.5 73 49.5 74 40.5 75 34.5 76 31.0 77 22.5 78 18.5 79 15.5 80 11.5 81 6.5 82 5.0 83 6.0 84 6.0 85 4.0 86 1.5 87 1.0 88 1.0 89 0.5 90 0.0 91 0.0 92 0.0 93 0.5 94 0.5 95 0.0 96 0.0 97 0.0 98 0.0 99 0.5 100 1.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.975 2 0.975 3 0.95 4 0.95 5 0.95 6 0.95 7 0.975 8 0.95 9 1.0 10-11 1.0375 12-13 1.0875 14-15 1.3125 16-17 1.3 18-19 1.15 20-21 1.225 22-23 1.2375 24-25 1.125 26-27 1.25 28-29 1.225 30-31 1.225 32-33 1.2625000000000002 34-35 1.2375 36-37 0.3028773346794548 38-39 0.2902940805250537 40-41 0.3029537995455693 42-43 0.3408230244887655 44-45 0.1767453604342886 46-47 0.22727272727272727 48-49 0.30303030303030304 50-51 0.21464646464646464 52-53 0.11366506693609499 54-55 0.1262945188178833 56-57 0.11366506693609499 58-59 0.21483634525464426 60-61 0.29069767441860467 62-63 0.1769464105156724 64-65 0.139099645928174 66-67 0.15184107301024927 68-69 0.12658227848101267 70-71 0.2281658004816834 72-73 0.1273560876209883 74-75 0.22911051212938005 76 0.15582391897156214 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 38.0 36 0.0 37 0.0 38 1.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 1.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 51 1.0 52 0.0 53 0.0 54 0.0 55 0.0 56 0.0 57 2.0 58 1.0 59 0.0 60 0.0 61 0.0 62 0.0 63 2.0 64 0.0 65 2.0 66 1.0 67 0.0 68 2.0 69 1.0 70 7.0 71 8.0 72 14.0 73 74.0 74 270.0 75 1008.0 76 2567.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.95 #Duplication Level Percentage of deduplicated Percentage of total 1 97.05107951553448 92.15 2 2.1590310689836754 4.1000000000000005 3 0.44760400210637175 1.275 4 0.105318588730911 0.4 5 0.105318588730911 0.5 6 0.07898894154818326 0.44999999999999996 7 0.02632964718272775 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.02632964718272775 0.95 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 38 0.95 No Hit TGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGAT 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 6 0.15 No Hit ATCGATTAATAGATAAAACTAAATATGAAGAAGGTCTAAATAAAAAGAAA 6 0.15 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAGATAAAACTAAATATGAAGAAGGTCT 6 0.15 No Hit CTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAAT 5 0.125 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 5 0.125 No Hit AATAGATAAAACTAAATATGAAGAAGGTCTAAATAAAAAGAAACAAAATA 5 0.125 No Hit ATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAGATAAAACTAAATATGAAGAAGGTCTAAATAAAA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 59 0.0 0.0 0.0 0.0 0.0 60 0.0 0.0 0.0 0.0 0.0 61 0.0 0.0 0.0 0.0 0.0 62 0.0 0.0 0.0 0.0 0.0 63 0.0 0.0 0.0 0.0 0.0 64 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra Read 1052408 spots for SRR11389769.sra Written 1052408 spots for SRR11389769.sra SRR ids: ['SRR11389769.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_u0v_5mcz SRR11389769.sra spots: 21048160 blocks: [[1, 1052408], [1052409, 2104816], [2104817, 3157224], [3157225, 4209632], [4209633, 5262040], [5262041, 6314448], [6314449, 7366856], [7366857, 8419264], [8419265, 9471672], [9471673, 10524080], [10524081, 11576488], [11576489, 12628896], [12628897, 13681304], [13681305, 14733712], [14733713, 15786120], [15786121, 16838528], [16838529, 17890936], [17890937, 18943344], [18943345, 19995752], [19995753, 21048160]] SRR11389769 file size 3994082 SRR11389769 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o SRR11389769 SRR11389769_1.fastq SRR11389769_2.fastq Input file: SRR11389769_1.fastq Paired file: SRR11389769_2.fastq trimmed: SRR11389769-trimmed-pair1.fastq, SRR11389769-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Sat Dec 7 05:38:31 2024 >> started Sat Dec 7 05:38:47 2024 >> done (16.494s) 21048160 read pairs processed; of these: 551 ( 0.00%) short read pairs filtered out after trimming by size control 236160 ( 1.12%) empty read pairs filtered out after trimming by size control 20811449 (98.88%) read pairs available; of these: 18823 ( 0.09%) trimmed read pairs available after processing 20792626 (99.91%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 478 0.00% 19 40 0.00% 20 531 0.00% 21 43 0.00% 22 567 0.00% 23 53 0.00% 24 639 0.00% 25 43 0.00% 26 668 0.00% 27 67 0.00% 28 551 0.00% 29 63 0.00% 30 524 0.00% 31 61 0.00% 32 346 0.00% 33 24 0.00% 34 259 0.00% 35 253 0.00% 36 714 0.00% 37 266 0.00% 38 470 0.00% 39 262 0.00% 40 359 0.00% 41 319 0.00% 42 429 0.00% 43 444 0.00% 44 511 0.00% 45 465 0.00% 46 577 0.00% 47 604 0.00% 48 634 0.00% 49 718 0.00% 50 797 0.00% 51 926 0.00% 52 976 0.00% 53 1112 0.01% 54 1240 0.01% 55 1403 0.01% 56 1839 0.01% 57 1922 0.01% 58 2048 0.01% 59 2202 0.01% 60 2371 0.01% 61 2624 0.01% 62 2855 0.01% 63 3424 0.02% 64 3929 0.02% 65 3831 0.02% 66 4452 0.02% 67 4951 0.02% 68 5095 0.02% 69 5489 0.03% 70 6577 0.03% 71 9706 0.05% 72 28697 0.14% 73 193479 0.93% 74 1482345 7.12% 75 9502340 45.66% 76 9522837 45.76% 20811449 reads passed initial QC criterion=sequence-density sequence-density=0.85 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=27 prefix-density=0.81 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.02 sequence-density-rank=28 fanout-score=45.13 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=12.3 sequence=AAAAAAAAAAGTATGTTTGCATCAATGATAATCCCAAAGTAGGAAGTGTGTACGTAGTAGCAAGTGTTATACATACATAAAATTAAGCGATGCGTTTCGATCAAGTACTTGGCATCATCGATCACATACGTACATTTCACAGCAGGTAGCTACGTACATTACAGGCATACGTACATGCAGAGAGATACCCGGCCCTGTGTTGTGTTTGCAATTGCATAGATGAGAATGAGATGACTTGATTCTTAATTAGCCGGCGAGAGCGCTGGTGTTGTAGACGAGGAGGGCGCCGCCGCCGAGGAGGCCGGCCAGGGTGACGGCCCAGATCAGGAGCCCCGTCGTCCCACCGGCGTAGCGGTCGCCAGATTCGGACCATACCTCCGGCGTGTAGATCGGGCTGTAGCCGTCGACGTTGGCGCCGTACTTGTCAACAAACTGGTACACACCCTTTCCCGTGCCCTTCCTGCCGTTGGCGTCGATGTCCACCGTCAAGCCACCTCCGATCCCGAGGGGC criterion=sequence-density sequence-density=0.48 sequence-density-rank=1 fanout-score=2.38 fanout-score-rank=22 prefix-density=0.50 prefix-fanout=2.3 sequence=CAGGTGCTCAAGGAGCTGGAGGAGGTCAAGAAGGAGTACCCGGACGCCTA criterion=fanout-score sequence-density=0.13 sequence-density-rank=20 fanout-score=72.93 fanout-score-rank=1 prefix-density=0.73 prefix-fanout=13.2 sequence=GCCGCCGCCGCC SRR11389769 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 05:39:51 Started mapping on | Dec 07 05:39:51 Finished on | Dec 07 05:42:39 Mapping speed, Million of reads per hour | 445.96 Number of input reads | 20811449 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 16638900 Uniquely mapped reads % | 79.95% Average mapped length | 150.02 Number of splices: Total | 5405725 Number of splices: Annotated (sjdb) | 5095268 Number of splices: GT/AG | 5334775 Number of splices: GC/AG | 58734 Number of splices: AT/AC | 1459 Number of splices: Non-canonical | 10757 Mismatch rate per base, % | 0.93% Deletion rate per base | 0.01% Deletion average length | 1.67 Insertion rate per base | 0.01% Insertion average length | 1.72 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3031834 % of reads mapped to multiple loci | 14.57% Number of reads mapped to too many loci | 74356 % of reads mapped to too many loci | 0.36% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.41% % of reads unmapped: other | 1.71% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1140745 1140745 1140745 N_multimapping 3031834 3031834 3031834 N_noFeature 810919 16047161 1008977 N_ambiguous 575814 3442 210169 UnstrandedReadsAssigned:15252167 PositiveStrandReadsAssigned:588297 NegativeStrandReadsAssigned:15419754 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389769 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR11389769-trimmed-pair1.fastq SRR11389769-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,811,449 reads, 18,037,043 reads pseudoaligned [quant] estimated average fragment length: 184.873 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,135 rounds 52973 SRR11389769.ke.tsv 35125 SRR11389769.se.tsv 88098 total ==> SRR11389769.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 752.23 0 0 PNS24247 1044 860.127 25.0042 2.02488 PNS24249 1928 1744.13 37.6711 1.50446 PNS24246 1044 860.127 25.0042 2.02488 PNS24248 1044 860.127 25.0042 2.02488 PNS24244 1471 1287.13 172.316 9.32512 PNS24243 293 120.69 0 0 KQK14069 1603 1419.13 1033.46 50.7249 KQK14071 474 291.625 15.8168 3.77782 ==> SRR11389769.se.tsv <== BRADI_1g14170v3 1089 BRADI_1g53295v3 24 BRADI_1g59795v3 226 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 112 BRADI_1g74790v3 155 BRADI_1g09890v3 0 BRADI_1g77505v3 265 BRADI_1g48960v3 0 SRR11389769 completed mapping pipeline successfully